Application of a Treg gene signature to measure disease trajectory and treatment response in type 1 diabetes

Insufficient regulatory T cell (Treg) control of autoreactive T cell-mediated destruction of beta-cells contributes to type 1 diabetes (T1D). Multiple therapeutic strategies to restore a normal immunoregulatory balance and stop T1D progression are in development and testing. However, a major challenge has been defining biomarkers that can prospectively identify subjects most likely to benefit from immunotherapy and/or measure intervention effects on immunity. We previously found that Tregs from children with new-onset T1D have an altered gene signature compared to healthy controls, suggesting that this could be a useful biomarker to monitor immunoregulation. Here we investigated whether the Treg gene signature is also altered in T1D adults, finding significant differences in new-onset and cross-sectional cohorts compared to controls (AUC=0.830, AUC=0.953). Furthermore, we also found that significant differences in the Treg gene signature are detected in unfractionated peripheral blood mononuclear cells, with statistical power increased by including genotype for T1D-associated SNPs (e.g. signature + Cd25 rs2104286 AUC=0.996). Treg gene signatures in T1D were distinct from those with T2D, indicating disease-specific Treg alterations. We further tested the predictive potential of the Treg gene signature by longitudinal testing in a phase I/II clinical trial of immunotherapy with ustekinumab (aIL-12/23p40). When looking at the change in Treg gene signature between weeks 0 and 40, we found an algorithm that could accurately discriminate between patients who had slow versus rapid c-peptide decline (AUC=0.818). Moreover, when examining data at week 40 alone there was a near perfect separation of slow versus rapid c-peptide decline subjects, possibly indicating a restoration of immunoregulatory balance in subjects who responded to ustekinumab. Overall these data confirm that Treg gene signature measurement is a simple and useful biomarker to measure immunoregulatory status and could possibly be useful for predicting disease trajectory, as well as stratifying and monitoring immunotherapy patients.